The document discusses the classification of bacteria. It covers the key taxonomic ranks used to classify bacteria, including identification, classification, and nomenclature. The criteria used to identify bacteria include growth on different media, microscopy, and biochemical and immunological tests. Nucleic acid-based tools are also discussed for bacterial taxonomy and classification. The major groups of bacteria - archaebacteria, eubacteria, and their subgroups - are outlined.

1. Classification of Bacteria

2. Reference: Jawetz, Melnick & Adelberg’s
MEDICAL MICROBIOLOGY
OBJECTIVES
1. Understand how the vocabulary of taxonomy is
critical to
communicating the science of infectious diseases.
2. Know the taxonomic ranks.
3. Appreciate the growth, biochemical, and genetic
characteristics that are used in differentiating bacteria.
4. Understand the differences between the eubacteria,
archaebacteria, and eukaryotes.
5. Understand the different tools for nucleic acid–
based
taxonomy.

3. There is a wide diversity of medical
pathogens that are associated with
infectious diseases in this world we live in.
The diversity of these identifiable pathogens
is so great that it is important to appreciate
the subtleties associated with each
infectious agent.

4. The reason for understanding these differences
is significant because each infectious agent
has specifically adapted to a particular mode(s)
of transmission, the capacity to grow in a
human host (colonization), and a mechanism(s)
to cause disease (pathology).

5. Identification, classification, and
nomenclature.
These three are separate but interrelated areas
of bacterial taxonomy.
Each area is critical to the ultimate goal of
accurately studying the infectious diseases and
precisely communicating these to others in the
field.

6. Identification
It is the practical use of a classification scheme
(1) Isolate and distinguish specific organisms
among the mix of complex microbial flora.
(2) Verify the authenticity or special properties
of a culture in a clinical setting.
(3) Isolate the causative agent of a disease.

7. For example, the popular literature has reported
Escherichia coli as the causative agent of hemolytic
uremic syndrome (HUS) in infants.
There are hundreds of different strains that are
classified as E. coli but only a few that are
associated with HUS.
These strains can be “identified” from the many
other
E. coli strains by antibody reactivity with their O-,
H-, and K-antigens.

8. E. coli H7:0157

9. Classification
It is the categorization of
organisms into taxonomic
groups.
Taxonomy is the science of
naming, describing and
classifying organisms and
includes all plants, animals
and microorganisms of the
world.

10. Nomenclature
Refers to the naming of an
organism by an established
group of scientific and medical
professionals.
Linnaean taxonomy is the
system most familiar to
biologists. It uses the formal
ranks of kingdom, phylum,
class, order, family, genus,
species, and subtype.

11. CRITERIA FOR IDENTIFICATION OF
BACTERIA
Growth on Media – One criterion is growth on
different types of bacteriologic media.
These media generally include agar, a carbon
source, and an acid hydrolysate or enzymatically
degraded source of biologic material (eg, casein).

12. Additionally, these types of media may be
supplemented by vitamins and even intact
red blood cells in the case of blood agar
media.
These types of media are referred to as
complex media.

13. A. Nonselective
Media
Blood agar and
chocolate agar are
examples of complex,
nonselective media,
which support the
growth of many
different bacteria. ( LB agar - Luria Broth)

14. B. Selective Media
Selective media is with an
incorporation of an
inhibitory agent that
specifically selects against
the growth of irrelevant
bacteria. Example:
Sodium azide selects for
Gram-positive bacteria
over Gram-negative
bacteria.

15. C. Differential Media
For example, pathogenic
salmonellae and shigellae
that do not ferment lactose
on a MacConkey plate form
white colonies, while
lactose fermenting
members of the
Enterobacteriaceae (eg, E.
coli) form red or pink
colonies.

16. OTHER TESTS
Microscopy - This is the
first step in identifying
individual microbial
specimens (eg, are they
Gram-negative or
Gram-positive) grown in
culture or even directly
from patient specimens
(eg, urine or cerebral
spinal fluids).

17. Biochemical Tests
Biochemical tests are the tests that are performed
on different bacteria for their identification on the
basis of their biochemical activities towards
different biochemical compounds.
Different biochemical tests are in your book in
Table 3-2.

18. Example 1: Catalase Test
The enzyme catalase
catalyzes the conversion of
hydrogen peroxide to water
and oxygen. When a colony is
placed in hydrogen peroxide,
liberation of oxygen as gas
bubbles can be seen. The test
is particularly useful in
differentiation of staphylococci
(positive) from streptococci
(negative).

19. Example 2: Coagulase Test
The enzyme coagulase acts with a plasma factor
to convert fibrinogen to a fibrin clot. It is used to
differentiate Staphylococcus aureus from other,
less pathogenic staphylococci
If the organism is demonstrated to be catalase
positive (Staphylococcus spp.), the species can
be subdivided by a coagulase test into
Staphylococcus aureus
(coagulase positive) or Staphylococcus
epidermidis (coagulase negative).

20. Coagulase positive
Coagulase negative

22. Ex. 3 Nitrate
reduction.
Bacteria may reduce
nitrates by several
mechanisms. This ability is
demonstrated by detection
of the nitrites and/or
nitrogen gas formed in the
process. This test is
included in a standard
urinalysis test to detect the
presence of Gram-negative
rods causing urinary tract

23. Immunologic Tests (Serotypes,
Serogroups, and Serovars)
The designation “sero” simply indicates the use of
antibodies that react with specific bacterial cell
surface structures such as lipopolysaccharide
(LPS), flagella, or capsular antigens.

24. Bacterial lipopolysaccharides (LPS) - major outer surface
membrane components present in almost all Gram-
negative bacteria and act as extremely strong
stimulators of innate or natural immunity in diverse
eukaryotic species ranging from insects to humans.

25. These immunologic tests link the source of an
organism to a disease caused in an individual. In
certain circumstances (eg, an epidemic), it is
important to distinguish among strains of a given
species or to identify a specific strain.
This is called subtyping and is accomplished by
examining bacterial isolates for characteristics that
allow discrimination below the species level.

26. For example, more than 130 serogroups of
Vibrio cholerae have been identified based
on antigenic differences in the O-
polysaccharide of their LPS; however, only the
O1 and O139 serogroups are associated with
epidemic and pandemic cholera.
Within these serogroups, only strains that
produce a toxin-coregulated pili and cholera
toxin are virulent and cause the disease
cholera.

27. By contrast, nontoxigenic V. cholerae strains,
which are not associated with epidemic
cholera, are generally isolated from
environmental specimens, from food, or from
patients with sporadic diarrhea.
Sporadic refers to a disease that occurs
infrequently and irregularly.

28. Endemic refers to the constant presence and/or
usual prevalence of a disease or infectious agent
in a population within a geographic area.
Epidemic is an outbreak of disease that spreads
quickly and affects many individuals at the same
time.
Pandemic is a disease outbreak that spreads
across countries or continents. It affects more
people and takes more lives than an epidemic.

29. Clonality with respect to isolates of microorganisms
from a common source outbreak (point source spread)
is an important concept in the epidemiology of
infectious diseases.
Clonality implies the state of a cell or a substance
being derived from one source or the other. Thus
there are terms like polyclonal—derived from many
clones; oligoclonal—derived from a few clones; and
monoclonal—derived from one clone.

30. Etiologic agents associated with these
outbreaks are the descendant of a single cell
and, for all practical purposes, are genetically
identical.
Subtyping plays an important role in
discriminating among these microorganisms.

31. Hybridoma technology
This has resulted in the development of
monoclonal antibodies against cell surface
antigens, which have been used to create
highly standardized antibody-based subtyping
systems that describe bacterial serotypes.

32. For example, some bacteria (eg, Neisseria
gonorrhoeae) or viruses (eg, human
immunodeficiency virus [HIV] and hepatitis C) are
transmitted as an inoculum composed of
quasispecies (meaning that there is extensive
antigenic variation among the bacteria present in
the inoculum).
In these cases, groups of hybridomas that
recognize variants of the original organisms are
used to categorize serovariants or serovars.

33. Genetic Diversity
Genetic Diversity refers to the range of different
inherited traits within a species. In a species
with high genetic diversity, there would be many
individuals/microorganism with a wide variety of
different traits.

34. Developments in DNA sequencing now make it
possible to investigate the relatedness of genes
or genomes by comparing sequences among
different bacteria.
Traits shared by all or none of the members of a
group cannot be used to distinguish its members,
but they may define a group (eg, all
staphylococci produce the enzyme catalase).

35. CLASSIFICATION SYSTEMS
Dichotomous Keys
Numerical Taxonomy Using Biochemical
Measures of Activity
Nucleic Acid–Based Taxonomy
- Plasmid Analysis
- Restriction Endonuclease Analysis
- Genomic Analysis
- Repetitive Sequence Analysis
- Ribosomal RNA sequencing
- Ribotyping

36. Dichotomous Keys
Dichotomous keys organize bacterial traits in
a manner that permits logical identification of
organisms. The ideal system should contain
the minimum number of features required for
a correct categorization.
Groups are split into smaller subgroups based
on the presence (+) or absence (−) of a
diagnostic character.

38. Numerical Taxonomy Using
Biochemical Measures of Activity
Numerical taxonomy became widely used in the
1970s. One example of this is the Analytical
Profile Index (API), which uses numerical
taxonomy to identify a wide range of medically
important microorganisms.

39. Analytical Profile Index APIs consist of several
plastic strips, each of which has about 20 miniature
compartments containing biochemical reagents.
Almost all cultivatable bacterial groups and
more than 550 different species can be identified
using the results of these API tests.

40. These identification
systems have extensive
databases of microbial
biochemical reactions.
The limitation of this
approach is that it is a
static system. As such, it
does not allow for the
evolution of bacteria and
routine discovery of new
bacterial
pathogens.

41. Nucleic Acid–Based Taxonomy
 1975
 started developments in nucleic acid isolation,
amplification, and sequencing.
 have spurred the evolution of nucleic acid–based
subtyping systems

42.  Includes: 1. Plasmid profile analysis
2. Restriction fragment endonuclease
analysis
3. Repetitive sequence analysis
4. Ribotyping
5.16S ribosomal sequencing
6. Genomic sequencing

43. 1. Plasmid Analysis
Plasmids are
extrachromosomal
genetic elements.
These can be isolated
from an isolated
bacterium and separated
by agarose gel
electrophoresis to
determine their number
and size.

44. Plasmids - genetic structure in a cell that can
replicate independently of the chromosomes,
typically a small circular DNA strand in the
cytoplasm of a bacterium or protozoan.
Plasmids are much used in the laboratory
manipulation of genes.

45. Plasmid analysis has been shown to be most
useful for examining outbreaks that are restricted
in time and place (eg, an outbreak in a hospital).
It is a rapid, convenient way to follow the spread
of the epidemic strain and may be more specific
than other typing methods.
Example event occurred during an outbreak of
Infection due to Methicillin resistant
Staphylococcus aureus.

46. 2. Restriction
Endonuclease
Analysis
This is one of the
most basic
procedures in
molecular biology. It
is inexpensive but
time consuming.

47. 3. Genomic Analysis
Genomic analysis is the identification, measurement or
comparison of genomic features such as DNA sequence,
structural variation, gene expression, or regulatory and
functional element annotation at a genomic scale.
The routine use of DNA genome sequencing allows the
precise comparison of divergent DNA sequences, which
can give a measure of their relatedness.

49. 4. Repetitive Sequence Analysis
Repeated sequences are patterns of nucleic acids (DNA or
RNA) that occur in multiple copies throughout the
genome.
A genotyping approach using polymerase chain reaction
(PCR), is used.
It has proved especially useful in subtyping monomorphic
species such as Bacillus anthracis, Yersinia pestis, and
Francisella.

50. 5. Ribosomal RNA sequencing
Ribosomes have an essential role in protein synthesis for
all organisms. Comparison of the nucleotide sequence
of 16S rRNA from a range of prokaryotic sources
revealed evolutionary relationships among widely
divergent organisms and has led to the discovery of a
new kingdom, the archaebacteria.
The phylogenetic tree based on rRNA sequencing data,
showed that bacteria, archaea, and eukaryote belong to
different families.

51. 6. Ribotyping
Ribotyping is a molecular method that takes advantage of
unique DNA sequences to differentiate strains of organisms.
This fragment-based technology utilizes restriction enzymes
to target and cut regions of the ribosomal RNA genes (5S,
16S, 23S and the spacer region including Glu-tRNA),
generating a DNA fingerprint that is unique to the organism
at the strain level.

53. DESCRIPTION OF THE MAJOR CATEGORIES
AND GROUPS OF BACTERIA
The definitive work on the taxonomic organization of
bacteria is the latest edition of Bergey’s Manual of
Systematic Bacteriology.
First published in 1923, this publication taxonomically
classifies, in the form of a key, known bacteria that have
or have not been cultured or well described.

54. A companion volume, Bergey’s Manual of
Determinative Bacteriology, serves as an aid in the
identification of bacteria that have been described
and cultured.
The major bacteria that cause infectious diseases, as
categorized in Bergey’s Manual, are listed in Table 3-3
in your book.

55. Eukaryotic cells are cells that contain a nucleus.
Eukaryotic cells have other organelles besides the
nucleus.
Prokaryotic cells are cells without a nucleus
The only organelles in a prokaryotic cell are
ribosomes.

56. There are two different groups of prokaryotic
organisms: eubacteria and archaebacteria. Both are
small unicellular organisms that replicate asexually.
Eubacteria refer to classic bacteria. They lack a true
nucleus, have characteristic lipids that make up their
membranes, possess a peptidoglycan cell wall, and
have a protein and nucleic acid synthesis machinery
that can be selectively inhibited by antimicrobial agents.

57. In contrast, Archaebacteria do not
have a classic peptidoglycan cell wall
and have many characteristics (eg,
protein synthesis and nucleic acid
replication machinery) that are similar to
those of eukaryotic cells.

60. The Eubacteria
A.Gram-Negative Eubacteria
 Heterogeneous group of bacteria
 Gram-negative type cell envelope
consisting of an outer membrane, a
periplasmic space containing a thin
peptidoglycan layer or cell wall, and a
cytoplasmic membrane.

61.  Cell shape may be spherical, oval, straight or
curved rods, helical, or filamentous; some of these
forms may be sheathed or encapsulated.
 Reproduction is by binary fission, budding. Fruiting
bodies and myxospores may be formed by the
myxobacteria.
 Motility, if present, occurs by means of flagella or
by gliding motility.
 May be phototrophic or nonphototrophic bacteria,
aerobic, anaerobic, facultatively anaerobic, and
microaerophilic species.

62. B. Gram-Positive Eubacteria
 Cell wall profile of the Gram-positive type; cells
generally, but not always, stain Gram-positive.
 Cell envelope of Gram-positive organisms
consists of a thick cell wall and a cytoplasmic
membrane.
 May be encapsulated and can exhibit flagellar-
mediated motility.

63.  May be spherical, rods, or filaments; the rods and
filaments may be nonbranching or may show true
branching.
 Reproduction is generally by binary fission. Some
bacteria may produce spores (eg, Bacillus and
Clostridium spp.) as resting forms that are highly
resistant to disinfection.
 The Gram-positive eubacteria are generally
chemosynthetic heterotrophs and include aerobic,
anaerobic, and facultatively anaerobic species

65. C. Eubacteria Lacking Cell Walls
 These are microorganisms that lack cell walls
(commonly called mycoplasmas and making up the class
Mollicutes) and do not synthesize the precursors of
peptidoglycan.
 They are enclosed by a unit membrane, the plasma
membrane.
 Six genera have been designated as mycoplasmas based
on their habitat; however, only two genera contain
animal pathogens.

66.  Mycoplasmas are highly pleomorphic and range in
sizes from vesicle-like forms to very small (0.2
μm), filterable forms (meaning that they are too
small to be captured on filters that routinely trap
most bacteria.
• Reproduction may be by budding, fragmentation,
or binary fission, singly or in combination.
 Most species require a complex medium for
growth and tend to form characteristic “fried egg”
colonies on a solid medium.

68. The Archaebacteria
 Predominantly inhabitants of extreme terrestrial and
aquatic environments (high salt, high temperature,
anaerobic) and are often referred to as extremophiles.
 Some are symbionts in the digestive tract of humans
and animals.
 The archaebacteria consist of aerobic, anaerobic, and
facultatively anaerobic organisms that are
chemolithotrophs, heterotrophs, or facultative
heterotrophs, and mesophiles.

69.  Others can grow at temperatures above 100°C.
These hyperthermophilic archaebacteria are
uniquely adapted for growth at high temperatures.
 Cells may have a diversity of shapes, including
spherical, spiral, and plate or rod shaped; unicellular
and multicellular forms in filaments or aggregates.
• Multiplication occurs by binary fission, budding,
constriction, fragmentation, or other unknown
mechanisms.

70. Halophiles are “salt-loving”.
Thermophilic bacteria loves high
temperatures, usually between 45
and 80 C (113 and 176F) and are
found in environments such as hot
springs, peat bogs, and near deep-
sea hydrothermal vents
Acidophiles thrives in acidic
natural (solfataric fields, sulphuric
pools) and man-made (eg. Acid
mine drainage) environments.

71. NONCULTURE METHODS FOR THE
IDENTIFICATION OF PATHOGENIC
MICROORGANISMS
This uses PCR (polymerase chain reaction) test which
utilizes the study of the ribosomal DNA and rRNA
sequences of the microorganism for identification.
Just like our present Covid infection. We use a real-time
reverse transcription polymerase chain reaction (rRT -
PCR) test.

72. UPDATES TO TAXONOMIC CHANGES
The technologic advances in the fields of
molecular genetics and microbiome research
have led to an explosion in the number of newly
identified species compared with the rate at which
they were discovered even a decade ago.
For medical microbiology, biennial updates to
the field of microbiology taxonomy are published
in the Journal of Clinical Microbiology.

73. We’ll be in Microbiology for one semester.
Happy studying and God bless!!!